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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttgttatccctgtgtcttcccttagggtttactgaaactttttcttatggctaattctggttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g18510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058138_T01 (Zea mays), 3'ss of exon 2
gttcttgttatccctgtgtcttcccttagggtttactgaaactttttcttatggctaattctggttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG
||||| |||  ||||||   |  ||||  | |||    |   | |||   |   |||||| |   ||  |||||||||||| |||| ||| ||||||||||| || |||||||||||||| ||||||||||| |||||||| |||||||||||||| ||||||||||| || ||||
gttctagttggccctgttggtgtccttgtgatttgacaatggtatttgcaaaaactaattgtatctgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAATTGTCCTGTGAAGATTAAACTAGTTGCTCCTCCACTTTATGTTCTGACCACACAGACCCTTG

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
gttcttgttatccctgtgtcttcccttagggtttactgaaacttttt-cttatggctaattctggttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG
||||| |||  ||||    |  |||||  | ||||   |   | ||| |  |   |||||| |   ||  |||||||||||| |||| ||| ||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||||||  |||||||||| || ||||
gttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaactaattgtatatgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G05470.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gttcttgttatc-cctgtgtcttcccttagggtttactgaaacttttt--cttatggctaattctggttggtt------------ttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG
          | ||| || |   |||| | ||   || |  ||  |||    ||||   ||| | |||||   || |||| |            || ||| ||||||||| |||||| || ||||  |||| |||| |||||||||| || || ||||| ||||| || ||||||||||| || || || || || | | 
gtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacagGAAGCCATGAAGAAGGCAGAGGCTGTAGGTACTGATGATTGTCCAGTCAAAATCAAGCTCGTTGCTCCACCACTTTATGTACTCACAACTCACACCCATT

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S55_319V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------gttcttgttatccctgtgtcttcccttagggtttactgaaactttttcttatggctaattctg--gttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG
                      ||| | |   |       |    |      ||||   |  | ||||  | |   |   ||||   ||  || || ||| | || ||||| ||||| || |||||||| | |||  | ||||| |||||||||||| |||| ||||| |||||||||||| | |||||||| || ||||
caacggtctgttactaaaaggagttttggcattaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29615907|gb|CB620919.1|CB620919
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|86495831|gb|CI138464.1|CI138464
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|86498995|gb|CI141628.1|CI141628
EST:     GATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: GATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|3767755|gb|AU031782.1|AU031782
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|4714850|gb|AU055967.1|AU055967
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         C
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcag-
EST: gi|4714850|gb|AU055967.1|AU055967
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         C
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcag-
EST: gi|29615906|gb|CB620918.1|CB620918
EST:     ATGTTTCCAATTTGATGGGGTGCTTCCCATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: ATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|86502170|gb|CI144803.1|CI144803
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|29615940|gb|CB620952.1|CB620952
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|87018064|gb|CI275878.1|CI275878
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAG                         CAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG
EST: gi|218497968|gb|FG969492.1|FG969492
EST:     CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTTACATTAAG                         CAAGCCATGAGGAAGGCTGA-GCTGCTGGTAATGATAATTGTCCAGTGAAG
genomic: CTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 44 (downstream exon)
Score: 31

AGTTAAGAATATAAGGAGGAGGATGACACCACAGCCACTTAAGATCCGTGCTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgtta ... ggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttagggtttactgaaactttttcttatggctaattctggttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG
                               ggctaat  putative branch site (score: 31)
                 aaactttttcttat  TA-rich tract